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Coexpression cluster:C205

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Full id: C205_mycosis_cord_hairy_xeroderma_CD4_B_b



Phase1 CAGE Peaks

  Short description
Hg19::chr10:110789709..110789714,- p@chr10:110789709..110789714
-
Hg19::chr10:89577732..89577739,- p13@ATAD1
Hg19::chr11:118075251..118075262,- p7@AMICA1
Hg19::chr11:35109970..35109983,+ p@chr11:35109970..35109983
+
Hg19::chr11:35110037..35110046,+ p@chr11:35110037..35110046
+
Hg19::chr11:73720276..73720286,- p2@UCP3
Hg19::chr12:104319259..104319279,+ p@chr12:104319259..104319279
+
Hg19::chr12:29165730..29165749,- p@chr12:29165730..29165749
-
Hg19::chr12:39299722..39299767,- p5@CPNE8
Hg19::chr12:68619488..68619503,- p3@IL26
Hg19::chr12:68619586..68619593,- p1@IL26
Hg19::chr12:81172256..81172287,+ p@chr12:81172256..81172287
+
Hg19::chr13:39462565..39462604,- p@chr13:39462565..39462604
-
Hg19::chr13:40880982..40881019,- p@chr13:40880982..40881019
-
Hg19::chr13:40881048..40881070,- p@chr13:40881048..40881070
-
Hg19::chr13:42968329..42968343,+ p@chr13:42968329..42968343
+
Hg19::chr13:50802126..50802138,+ p@chr13:50802126..50802138
+
Hg19::chr14:22355984..22355994,+ p2@TRAV12-2
Hg19::chr14:22356029..22356043,+ p1@TRAV12-2
Hg19::chr14:22356073..22356080,+ p3@TRAV12-2
Hg19::chr14:22356128..22356162,+ p4@TRAV12-2
Hg19::chr14:22356420..22356461,+ p1@AB305742
p1@AF532837
p1@AF532838
p1@AF532839
p1@AF532840
p1@AF532841
p1@AF532842
p1@AF532843
p1@AF532844
p1@AF532845
p1@AF532847
p1@AF532848
p1@AF532849
p1@AF532850
p1@AF532851
p1@AF532852
p1@AF532853
p1@AF532854
p1@AF532856
p1@AY135832
p1@AY135833
p1@AY135834
p1@AY135835
p1@AY135836
p1@AY135837
p1@AY135838
p1@AY135839
p1@AY135840
p1@AY135841
p1@AY135842
p1@AY135843
p1@AY135844
p1@AY135846
p1@AY135847
p1@AY135849
p1@AY135850
p1@AY135851
p1@AY135852
p1@AY135853
p1@EU340840
p1@M17652
p1@M17653
p1@M27369
p1@S82064
p1@X04940
p1@X04946
p1@X92766
p1@X92783
p1@X92883
Hg19::chr14:51651959..51651967,- p@chr14:51651959..51651967
-
Hg19::chr14:65803148..65803157,+ p@chr14:65803148..65803157
+
Hg19::chr14:65803162..65803174,+ p@chr14:65803162..65803174
+
Hg19::chr14:82495120..82495125,- p@chr14:82495120..82495125
-
Hg19::chr15:45174767..45174793,- p@chr15:45174767..45174793
-
Hg19::chr16:10912591..10912602,- p10@FAM18A
Hg19::chr16:11301790..11301804,+ p1@AK127887
Hg19::chr16:11301814..11301825,+ p2@AK127887
Hg19::chr16:28996572..28996586,+ p6@LAT
Hg19::chr17:32687516..32687555,- p@chr17:32687516..32687555
-
Hg19::chr17:32690382..32690387,- p2@CCL1
Hg19::chr17:32690435..32690446,- p3@CCL1
Hg19::chr18:56816533..56816576,+ p@chr18:56816533..56816576
+
Hg19::chr19:35476657..35476668,+ p@chr19:35476657..35476668
+
Hg19::chr19:35492016..35492027,+ p@chr19:35492016..35492027
+
Hg19::chr19:35492031..35492059,+ p@chr19:35492031..35492059
+
Hg19::chr19:4229557..4229568,+ p1@CU677281
Hg19::chr19:4229572..4229583,+ p2@CU677281
Hg19::chr1:1148422..1148468,- p@chr1:1148422..1148468
-
Hg19::chr1:1149506..1149515,- p2@TNFRSF4
Hg19::chr1:1173212..1173215,- p@chr1:1173212..1173215
-
Hg19::chr1:93043060..93043065,- -
p@chr1:93043060..93043065
Hg19::chr1:93043102..93043113,- p@chr1:93043102..93043113
-
Hg19::chr1:93043161..93043170,- p@chr1:93043161..93043170
-
Hg19::chr1:98642709..98642713,- p@chr1:98642709..98642713
-
Hg19::chr20:44692500..44692506,- p@chr20:44692500..44692506
-
Hg19::chr21:36430055..36430067,+ p@chr21:36430055..36430067
+
Hg19::chr21:43826483..43826494,- p@chr21:43826483..43826494
-
Hg19::chr21:43826497..43826511,- p@chr21:43826497..43826511
-
Hg19::chr2:160760800..160760805,+ p2@AK125488
Hg19::chr2:53979000..53979012,- p@chr2:53979000..53979012
-
Hg19::chr3:140980521..140980532,+ p9@ACPL2
Hg19::chr3:16412407..16412418,- p10@RFTN1
Hg19::chr3:186194261..186194278,+ p1@ENST00000456535
Hg19::chr3:186194280..186194291,+ p2@ENST00000456535
Hg19::chr3:189026010..189026019,+ p@chr3:189026010..189026019
+
Hg19::chr4:2934426..2934445,- p8@MFSD10
Hg19::chr5:107253874..107253881,- p@chr5:107253874..107253881
-
Hg19::chr5:107253962..107253972,- p@chr5:107253962..107253972
-
Hg19::chr5:131541116..131541121,- p@chr5:131541116..131541121
-
Hg19::chr6:100604462..100604467,- -
p@chr6:100604462..100604467
Hg19::chr6:128134176..128134183,- p10@THEMIS
Hg19::chr6:31540488..31540521,+ p2@LTA
Hg19::chr6:31541252..31541272,+ p@chr6:31541252..31541272
+
Hg19::chr6:31541315..31541329,- p1@CU689955
Hg19::chr7:109650548..109650592,+ p@chr7:109650548..109650592
+
Hg19::chr7:109650713..109650723,+ p@chr7:109650713..109650723
+
Hg19::chr7:142511059..142511075,- p2@TRBV30
Hg19::chr8:124008167..124008169,+ p@chr8:124008167..124008169
+
Hg19::chr8:29351739..29351773,+ p@chr8:29351739..29351773
+
Hg19::chr8:42037604..42037608,- p@chr8:42037604..42037608
-
Hg19::chr9:87359709..87359717,+ p@chr9:87359709..87359717
+
Hg19::chr9:92116537..92116544,- p@chr9:92116537..92116544
-
Hg19::chr9:92116561..92116575,- p@chr9:92116561..92116575
-
Hg19::chr9:93728939..93728974,- p@chr9:93728939..93728974
-
Hg19::chr9:93917134..93917162,- p@chr9:93917134..93917162
-


Enriched pathways on this co-expression clusterSummary:
Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.
Analyst: Emmanuel Dimont

link to source dataset
data


p.valueFDRnGenesnPathwayName
1.21026995633836e-050.00766100882362184265Cytokine-cytokine receptor interaction (KEGG):04060



Enriched Gene Ontology terms on this co-expression clusterSummary: Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0006955immune response0.000349807746282106
GO:0002376immune system process0.000426313808965761
GO:0019722calcium-mediated signaling0.00630455178790549
GO:0005125cytokine activity0.00973443726723401
GO:0051952regulation of amine transport0.0168129406759757
GO:0002036regulation of L-glutamate transport0.0168129406759757
GO:0051953negative regulation of amine transport0.0168129406759757
GO:0051956negative regulation of amino acid transport0.0168129406759757
GO:0002037negative regulation of L-glutamate transport0.0168129406759757
GO:0051955regulation of amino acid transport0.0168129406759757
GO:0005615extracellular space0.0168129406759757
GO:0009605response to external stimulus0.0247994292453115
GO:0007267cell-cell signaling0.0247994292453115
GO:0046325negative regulation of glucose import0.0252186099539889
GO:0048535lymph node development0.0271409218658873
GO:0050806positive regulation of synaptic transmission0.0271409218658873
GO:0001775cell activation0.0271409218658873
GO:0051971positive regulation of transmission of nerve impulse0.0271409218658873
GO:0043303mast cell degranulation0.0271409218658873
GO:0002448mast cell mediated immunity0.0271409218658873
GO:0045576mast cell activation0.0271409218658873
GO:0043299leukocyte degranulation0.0271409218658873
GO:0046323glucose import0.0271409218658873
GO:0046324regulation of glucose import0.0271409218658873
GO:0031646positive regulation of neurological process0.0271409218658873
GO:0005031tumor necrosis factor receptor activity0.0271409218658873
GO:0043525positive regulation of neuron apoptosis0.0273704643242504
GO:0002444myeloid leukocyte mediated immunity0.0273704643242504
GO:0043120tumor necrosis factor binding0.0273704643242504
GO:0044421extracellular region part0.027743861225859
GO:0005035death receptor activity0.027743861225859
GO:0016021integral to membrane0.027743861225859
GO:0031224intrinsic to membrane0.027743861225859
GO:0051222positive regulation of protein transport0.027743861225859
GO:0019932second-messenger-mediated signaling0.027743861225859
GO:0051239regulation of multicellular organismal process0.0285894817718104
GO:0045840positive regulation of mitosis0.0285894817718104
GO:0006954inflammatory response0.028644406585695
GO:0015813L-glutamate transport0.028644406585695
GO:0015800acidic amino acid transport0.028644406585695
GO:0005102receptor binding0.030947997828804
GO:0050804regulation of synaptic transmission0.033559563047681
GO:0009612response to mechanical stimulus0.0340307536623605
GO:0001772immunological synapse0.0340307536623605
GO:0051969regulation of transmission of nerve impulse0.0352261380904179
GO:0044459plasma membrane part0.0354480104691158
GO:0016020membrane0.0372626362680686
GO:0005886plasma membrane0.0372626362680686
GO:0044425membrane part0.0422303467262425
GO:0045787positive regulation of progression through cell cycle0.0422303467262425
GO:0031644regulation of neurological process0.0422911808133526
GO:0043523regulation of neuron apoptosis0.0422911808133526
GO:0009611response to wounding0.0439685993139882
GO:0002274myeloid leukocyte activation0.0439685993139882
GO:0051223regulation of protein transport0.0447607868065524
GO:0007585respiratory gaseous exchange0.0453502471319412
GO:0051402neuron apoptosis0.0453502471319412
GO:0015758glucose transport0.0453502471319412
GO:0051051negative regulation of transport0.0453502471319412
GO:0008645hexose transport0.0453502471319412
GO:0015749monosaccharide transport0.0453502471319412
GO:0003993acid phosphatase activity0.0453502471319412



Enriched sample ontology terms on this co-expression clusterSummary:To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
circulating cell2.22e-596
T cell2.20e-0725
pro-T cell2.20e-0725
Uber Anatomy
Ontology termp-valuen
umbilical cord4.37e-3610
blastocyst4.37e-3610
blastula4.37e-3610
bilaminar disc4.37e-3610
inner cell mass4.37e-3610
cleaving embryo4.37e-3610
connecting stalk4.37e-3610
inner cell mass derived epiblast4.37e-3610
extraembryonic mesoderm4.37e-3610
blood2.09e-2415
haemolymphatic fluid2.09e-2415
organism substance2.09e-2415
extraembryonic structure1.31e-1524
Disease
Ontology termp-valuen
non-Hodgkin lymphoma6.62e-411
cutaneous T cell lymphoma6.62e-411
mycosis fungoides6.62e-411


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary:The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.11.95874e-07
MA0004.10.10231
MA0006.10.0938208
MA0007.10.341929
MA0009.10.448088
MA0014.15.13523e-06
MA0017.10.256839
MA0019.10.113899
MA0024.10.0951076
MA0025.11.19671
MA0027.11.54867
MA0028.10.205854
MA0029.10.338623
MA0030.10.32489
MA0031.10.915926
MA0038.10.409705
MA0040.10.345724
MA0041.10.00812344
MA0042.10.0910969
MA0043.10.146285
MA0046.10.433494
MA0048.10.00488908
MA0050.10.198835
MA0051.10.400746
MA0052.10.108153
MA0055.10.00405477
MA0056.10
MA0057.10.017226
MA0058.10.0946498
MA0059.11.56178
MA0060.10.0574254
MA0061.11.96205
MA0063.10
MA0066.10.673164
MA0067.10.355517
MA0068.10.0114919
MA0069.10.42837
MA0070.10.41362
MA0071.10.330845
MA0072.10.407748
MA0073.10.308221
MA0074.10.206624
MA0076.10.111339
MA0077.10.793304
MA0078.11.40669
MA0081.10.184759
MA0083.10.150174
MA0084.10.506143
MA0087.10.404567
MA0088.10.284553
MA0089.10
MA0090.10.127884
MA0091.10.222341
MA0092.10.16619
MA0093.10.0448186
MA0095.10
MA0098.10
MA0100.10.715126
MA0101.12.44401
MA0103.10.156866
MA0105.10.259985
MA0106.13.74474
MA0107.12.91011
MA0108.20.24885
MA0109.10
MA0111.10.144556
MA0113.10.540252
MA0114.10.793845
MA0115.10.298932
MA0116.10.855002
MA0117.10.166938
MA0119.10.275406
MA0122.10.536553
MA0124.10.269645
MA0125.11.15261
MA0130.10
MA0131.10.0438471
MA0132.10
MA0133.10
MA0135.10.489695
MA0136.10.222134
MA0139.10.537831
MA0140.10.163149
MA0141.10.940702
MA0142.10.477603
MA0143.10.123194
MA0144.11.93475
MA0145.10.0192615
MA0146.10.0608306
MA0147.10.144203
MA0148.10.449634
MA0149.10.0115789
MA0062.20.095547
MA0035.20.546989
MA0039.20.0059725
MA0138.20.153619
MA0002.20.43546
MA0137.20.969917
MA0104.20.101682
MA0047.20.763779
MA0112.20.186156
MA0065.20.884499
MA0150.10.231127
MA0151.10
MA0152.10.338465
MA0153.10.587837
MA0154.10.948302
MA0155.10.353434
MA0156.10.0598773
MA0157.10.75061
MA0158.10
MA0159.10.145437
MA0160.10.750004
MA0161.10
MA0162.14.90804e-05
MA0163.10.130145
MA0164.11.29468
MA0080.20.849561
MA0018.20.271204
MA0099.21.19805
MA0079.20.000150439
MA0102.20.53771
MA0258.10.632921
MA0259.10.258665
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#10538123.747354121892877.91095060496588e-050.00121198734081272
BCL11A#5333593.273398665800810.001699693191511390.0106175164320987



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data